Fixed pedigree file input from user
More autobuild, bug fixes

-Fixed bug ignoring -pedigree cmd input
- Autobuild of AnnovarDbs
- AutoBuild of human reference “.dict” and “.fasta.fai” files
- exchanged samtoolsSort for PicardTools SortSam
- Changed VALIDATION_STRINGENCY from LENIENT to STRICT in Markduplicates
- Updated PicardVersion to 1.106
- Added Bam to SAM and SAM to BAM conversion using Picard since MOSAIK does not set the correct bin field by default.
- Added generalised picardTool tempDir i.e. changed name of flag “PicardToolsMergeTempDirectory" to “PicardToolsTempDirectory”
- Added 1000G high confidence resource to GATKVariantrecalibration
Bumped version number
Merge branch 'release/v1.4.8'